May be you can use the shared file of older document with the newer one and try if you can bring all the information regarding user selections back for newer file. Alternatively you can avoid such problems by keeping both Prod and QA files sync.

When I say both the files sync it means both QA and PROD files are synchronized and having same updated information after deployment. But as you have mentioned you replace PROD file by newer QA file, rather doing any changes directly onto the PROD version, there should not be any problem.